Research workbench
Crystal structure of a pyridoxamine kinase from yersinia pestis CO92
Analyse Crystal structure of a pyridoxamine kinase from yersinia pestis CO92 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PZS
- Type
- protein
- Length
- 571 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyridoxamine kinase
- EC
- 2.7.1.35
- UniProt
- Q7CIR8
- Ligands
- NA, SO4
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyridoxamine kinase (EC 2.7.1.35) | protein | 285 | 43% helix, 20% strand | Q7CIR8 |
| B | Pyridoxamine kinase (EC 2.7.1.35) | protein | 286 | 43% helix, 20% strand | Q7CIR8 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- BME · Beta-mercaptoethanol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 449 | 0.75 | 0.84 | 60 | SO4 |
| 2 | 501 | 0.73 | 0.81 | 56 | SO4 |
| 3 | 63 | 0.49 | 0.85 | 16 | BME |
| 4 | 88 | 0.45 | 0.81 | 22 | BME |
Interfaces
1 interface between chains.
- A–B · 1837 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 modified (engineered).
Compared structures
- 3PZS · Crystal Structure of a pyridoxamine kinase from Yersinia pestis CO92 · the same entry in another collection · chain A against A, TM-score 1.00
- Q7CIR8 · AlphaFold monomer V2.0 prediction for pyridoxal kinase pdxy (Q7CIR8) · a predicted model of the same protein · chain B against A, TM-score 0.98
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q7CIR8
- Elsewhere: RCSB PDB 3PZS · PDBe 3PZS · UniProt Q7CIR8
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